The national popular vote is a summation of independent state popular votes for their respective slates of electors to the Electoral College. The electors, in turn, vote for the President.
Since the people do not vote directly for the President, there is no issue with equal protection because their vote is protected within their states when they vote for their desired slate of electors to the Electoral College.
-PJ
All one would have to do is call into question any states count of the vote.
There is a huge issue. Even the nonsense that happened in 2000 was an equal protection issue; as counties (namely democrap ones) came up with different ideas on what a chad was, the SCOTUS ruled for it to stop.